A computational framework for quantitative set analysis of gene expression. QuSAGE accounts for inter-gene correlations, improves the estimation of the variance inflation factor and, rather than evaluating the deviation from a null hypothesis with a P-value, it quantifies gene-set activity with a complete probability density function. From this probability density function, P-values and confidence intervals can be extracted and post hoc analysis can be carried out while maintaining statistical traceability. Compared with Gene Set Enrichment Analysis and CAMERA, QuSAGE exhibits better sensitivity and specificity on real data profiling the response to interferon therapy (in chronic Hepatitis C virus patients) and Influenza A virus infection.

[…] after filtering, the lmfit and ebayes functions were used to perform moderated paired t testing for each gene across visits 1 and 2., at this level, gene set enrichment of isg was performed with the qusage package in r [], comparing our processed gene lists against those from a prior study of a549 cell lines subjected to α or γ interferon []., genes of interest from either group […]

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[…] between expressed genes in the aged vs. young ldlr −/− mice maintained on a chow diet compared to the other groups (fig. s7). thus, we focused on this group for our gene set analysis using qusage gene set enrichment analysis., we observed that gene sets that were upregulated within the aorta with aging included viral invasion and host response, platelet adhesion; and extracellular […]

[…] san diego, ca). illumina arrays were log-transformed and quantile-normalized by using lumi package []. the normalized expression levels were used to find activity of tfs and signaling pathways using qusage [, ]. the target genes of tfs and the genes involved in the pathways were obtained from msigdb []. particularly, gene-sets for ligand induced signaling pathways were obtained from biocarta, […]

[…] center for advancing translational science (ncats) ucla ctsi grant number ul1tr000124, and nih t32hl072752 (to yt). the authors would like to thank christopher bolen phd for his assistance with the qusage function […]

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